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Information on software used, (or which could be used) at CMIC. Information on software used, (or which could be used) at CMIC.
 +* [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.
* [http://cmicdev.cs.ucl.ac.uk/trac/ vtkCmic] Mark and David's classes for registration etc. * [http://cmicdev.cs.ucl.ac.uk/trac/ vtkCmic] Mark and David's classes for registration etc.
* [[Fluid Registration]] Details about Bill Crum's fluid implementation and related tools. * [[Fluid Registration]] Details about Bill Crum's fluid implementation and related tools.

Revision as of 01:07, 2 August 2007

This is the UCL Centre for Medical Image Computing (CMIC) wiki. The official CMIC webpage is here.

Contents

The CMIC Group

Administration

For any queries regarding the administration of CMIC please contact Dominique Drai on Ext. 31320 betweeen 09:30 and 13:30. Dominique is located in room 4.13

Requests for a Wiki user name and password should be sent to Ron.

Holiday request form Media:leave-form.pdf

Room bookings: CS UCL Med Phys

People

People at CMIC. Please enter your phone numbers, email address, room number, and whatever else at this address. There's also a staff page on the external website which is useful for finding contact details.

PhD

PhD Pages Information specific to CMIC PhD students.

Seminars and Reading Groups

Information on seminars at CMIC.

  • ImPr Pages Informal seminars on image processing.

Software

Information on software used, (or which could be used) at CMIC.

  • Camino Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.
  • vtkCmic Mark and David's classes for registration etc.
  • Fluid Registration Details about Bill Crum's fluid implementation and related tools.
  • Matlab Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc.
  • VTK C++ visualisation classes (some sort of interface to OpenGL).
  • Insight Toolkit (ITK) C++ imaging and image processing, registration, algorithms classes.
  • ITK++ C++ Daniel and Julia's image processing and registration classes
  • TNT C++ templated matrix classes.
  • TOAST Martin and Simon's finite element solvers and tools in C++.
  • SPM Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images.
  • FSL Similar toolbox/library written in C/C++. Popular tools include FLIRT, BET, and FAST.
  • FreeSurfer Cortical surface extraction, sub-cortical structure segmentation and inter-subject registration
  • (FreeSurfer includes N3 bias correction)
  • gxv, DisplayVectorField2D, DisplayVectorField3D GIPL X Viewers. Programs to enable display of up to 3 images and overlayed vector fields.
  • Plus see the list at Structural-Neuro#Useful_Neuro_Software.
  • Image File Formats Software available to read and manipulate image file formats and DICOM images in particular.
  • FAQ
  • Nifti
  • Misc. General (not medical-imaging) tools, e.g. Bibliography software, PDF tools, etc.
  • SSH
  • Virtual Network Computing (VNC) Desktop sharing system, for remote working, demos etc.
  • New CMIC Wiki Discussion on a new CMIC Wiki / web pages

Projects

Pages for specific projects at CMIC.

Science-div

Useful links

Ethics

Deadlines

  • Deadlines - Details of upcoming conference deadlines.

Undergraduate and MSc Projects

UGprojectDA on Parallel computing for the reconstruction of magnetic resonance images.

Postgraduate

Reading Material

Reading Material (publicly readable)

Please see documentation on customizing the interface and the User's Guide for usage and configuration help.

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